Add work of Thomas Durantel

Anima/diffusion/odf/CMakeLists.txt

@@ -1,2 +1,4 @@
 add_subdirectory(generalized_fa)
-add_subdirectory(odf_estimator)
+add_subdirectory(odf_estimator)
+add_subdirectory(tod_estimator)
+add_subdirectory(odf_average)

Anima/diffusion/odf/odf_average/CMakeLists.txt

@@ -0,0 +1,29 @@
+if(BUILD_TOOLS)
+
+  project(animaODFAverage)
+
+  # ############################################################################
+  # List Sources
+  # ############################################################################
+
+  list_source_files(${PROJECT_NAME} ${CMAKE_CURRENT_SOURCE_DIR})
+
+  # ############################################################################
+  # add executable
+  # ############################################################################
+
+  add_executable(${PROJECT_NAME} ${${PROJECT_NAME}_CFILES})
+
+  # ############################################################################
+  # Link
+  # ############################################################################
+
+  target_link_libraries(${PROJECT_NAME} ${ITKIO_LIBRARIES} AnimaSHTools)
+
+  # ############################################################################
+  # install
+  # ############################################################################
+
+  set_exe_install_rules(${PROJECT_NAME})
+
+endif()

Anima/diffusion/odf/odf_average/animaODFAverage.cxx

@@ -0,0 +1,136 @@
+#include <animaODFAverageImageFilter.h>
+#include <animaReadWriteFunctions.h>
+
+#include <fstream>
+
+#include <itkTimeProbe.h>
+
+#include <tclap/CmdLine.h>
+
+// Update progression of the process
+void eventCallback(itk::Object *caller, const itk::EventObject &event, void *clientData)
+{
+    itk::ProcessObject *processObject = (itk::ProcessObject *)caller;
+    std::cout << "\033[K\rProgression: " << (int)(processObject->GetProgress() * 100) << "%" << std::flush;
+}
+
+int main(int argc, char **argv)
+{
+    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ', ANIMA_VERSION);
+
+    TCLAP::ValueArg<std::string> inArg(
+        "i", "input-odf-file",
+        "A path or file name specifying the text file in which the ODF images are listed.",
+        true, "", "odf image list", cmd);
+    TCLAP::ValueArg<std::string> weightArg(
+        "w", "input-weight-file",
+        "A path or file name specifying the text file in which the weight images are listed.",
+        true, "", "weight image list", cmd);
+    TCLAP::ValueArg<std::string> outArg(
+        "o", "output-file",
+        "A path or file name specifying the output average ODF image.",
+        true, "", "output odf image", cmd);
+
+    TCLAP::ValueArg<unsigned int> nbpArg(
+        "T", "nb-threads",
+        "An integer value specifying the number of threads to run on (default: all cores).",
+        false, itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads(), "number of threads", cmd);
+
+    try
+    {
+        cmd.parse(argc, argv);
+    }
+    catch (TCLAP::ArgException &e)
+    {
+        std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    itk::CStyleCommand::Pointer callback = itk::CStyleCommand::New();
+    callback->SetCallback(eventCallback);
+
+    std::ifstream odfFile(inArg.getValue().c_str());
+    if (!odfFile.is_open())
+    {
+        std::cerr << "Please provide usable file with input ODFs" << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    std::ifstream weightFile(weightArg.getValue().c_str());
+    if (!weightFile.is_open())
+    {
+        std::cerr << "Please provide usable file with input weight images" << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    using FilterType = anima::ODFAverageImageFilter;
+    using InputImageType = FilterType::InputImageType;
+    using OutputImageType = FilterType::OutputImageType;
+    using WeightImageType = FilterType::WeightImageType;
+
+    FilterType::Pointer mainFilter = FilterType::New();
+
+    std::vector<std::string> inputFiles;
+    std::vector<std::string> weightFiles;
+
+    while (!odfFile.eof())
+    {
+        char tmpStr[2048], weightStr[2048];
+
+        odfFile.getline(tmpStr, 2048);
+        if (odfFile.fail())
+        {
+            std::cerr << "Error: Failed to read an ODF image." << std::endl;
+            return EXIT_FAILURE;
+        }
+
+        weightFile.getline(weightStr, 2048);
+        if (weightFile.fail())
+        {
+            std::cerr << "Error: Failed to read a weight image." << std::endl;
+            return EXIT_FAILURE;
+        }
+
+        if (strcmp(tmpStr, "") == 0 || strcmp(weightStr, "") == 0)
+            continue;
+
+        inputFiles.push_back(tmpStr);
+        weightFiles.push_back(weightStr);
+    }
+
+    odfFile.close();
+    weightFile.close();
+
+    unsigned int numInputs = weightFiles.size();
+
+    for (unsigned int i = 0; i < numInputs; ++i)
+    {
+        mainFilter->SetInput(i, anima::readImage<InputImageType>(inputFiles[i]));
+        mainFilter->AddWeightImage(i, anima::readImage<WeightImageType>(weightFiles[i]));
+    }
+
+    mainFilter->AddObserver(itk::ProgressEvent(), callback);
+    mainFilter->SetNumberOfWorkUnits(nbpArg.getValue());
+
+    itk::TimeProbe tmpTimer;
+
+    tmpTimer.Start();
+
+    try
+    {
+        mainFilter->Update();
+    }
+    catch (itk::ExceptionObject &e)
+    {
+        std::cerr << e << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    tmpTimer.Stop();
+
+    std::cout << "\nAveraging done in " << tmpTimer.GetTotal() << "s" << std::endl;
+
+    anima::writeImage(outArg.getValue(), mainFilter->GetOutput());
+
+    return EXIT_SUCCESS;
+}